RGD Reference Report - Microarray comparative genomic hybridization detection of copy number changes in desmoplastic melanoma and malignant peripheral nerve sheath tumor. - Rat Genome Database

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Microarray comparative genomic hybridization detection of copy number changes in desmoplastic melanoma and malignant peripheral nerve sheath tumor.

Authors: Pryor, JG  Brown-Kipphut, BA  Iqbal, A  Scott, GA 
Citation: Pryor JG, etal., Am J Dermatopathol. 2011 Dec;33(8):780-5. doi: 10.1097/DAD.0b013e31820dfcbf.
RGD ID: 9587769
Pubmed: PMID:21785329   (View Abstract at PubMed)
DOI: DOI:10.1097/DAD.0b013e31820dfcbf   (Journal Full-text)

Desmoplastic melanoma (DM) and malignant peripheral nerve sheath tumor (MPNST) can appear morphologically and immunophenotypically similar. We attempted to determine whether microarray comparative genomic hybridization could detect copy number differences between them to aid in the diagnosis. S-100 immunohistochemistry was performed on 5 cases of DM and 9 cases of MPNST using formalin-fixed paraffin-embedded specimens. Genomic DNA was extracted from microdissected cells. Whole genome amplification was performed on 5 of 5 DMs and 6 of 9 MPNST cases. A multiplex polymerase chain reaction assay was used to determine the quality of the DNA samples, which were run on the Spectral Chip 2600 bacterial artificial chromosome array platform. DM showed gains involving chromosomes 1p, 2p, 9q, 13q, 14q, and 20q and losses involving chromosomes 5p, 11p, 12q, 15q, and 18q. Several cancer-associated genes were involved, including gain of BCL2L1, ARTN, AMPK, NRAS, and CCNA1 and loss of IGF2, CDKN1C, PAX6, WT1, TRAF6, MAPK8IP1, and IMP3. MPNST had gains involving chromosomes 1p, 2q, and 19p and loss of chromosome 21q. Gains of MUM1, APC2, MAP2K2, JMJD2B, SP110, PTMA, GPI, and CDKN2D were detected. DM and MPNST have chromosomal alterations detected by array comparative genomic hybridization that might be useful in distinguishing these 2 tumors, although further studies with a larger sample size will be needed to test this.

RGD Manual Disease Annotations    Click to see Annotation Detail View
TermQualifierEvidenceWithReferenceNotesSourceOriginal Reference(s)
malignant peripheral nerve sheath tumor  IAGP 9587769DNA:amplification:cds (human)RGD 
malignant peripheral nerve sheath tumor  ISOKDM4B (Homo sapiens)9587769; 9587769DNA:amplification:cds (human)RGD 

Objects Annotated

Genes (Rattus norvegicus)
Kdm4b  (lysine demethylase 4B)

Genes (Mus musculus)
Kdm4b  (lysine (K)-specific demethylase 4B)

Genes (Homo sapiens)
KDM4B  (lysine demethylase 4B)


Additional Information